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If you add 5.5mm to these figures (tripod mount to sensor plane distance), you get the distance of the entrance pupil of the lens from the camera sensor plane (marked on the camera body by a small circle with a line through it). If you can measure on the 6D the distance between the sensor mark and the centre of the tripod mount screw, subtract this from the entrance pupil to sensor distances to get the upper rail settings for the 6D.

However, you can measure the settings yourself in half an hour with simple parallax checks using live view. The lower rail setting can be set by pointing the camera vertically down and adjust the rail position to bring the viewfinder's centre focus spot over the centre point of the rotator screw. Settings thus obtained will be quite adequate for most purposes, but can be refined by reference to these tutorials:

Thank you for your advice, after much testing. I got something good, but my pan head is not circular, but when I shoot down, the center of the photo (red dot) is almost in the center of NN4. I have some connections that are not good in the tiles but the rest of the panoramic picture is good.
Would you have any advice for fine settings?

Place the camera on your rig. Set F to max. Pitch down till you see the corner of your panohead. Focus to it. Now take you shots around. Import pics to PTGuiPro. Align pics. Go to "advanced" . Set minimize distorsion to "heavy and lens shift" and optimize. Del worst control points.
Set panorama settings to 360x180 and "create panorama" with a mov file. Move down to the nadir and have a look to your panohead circle.

You should end up with a set of three: One cuts to the right, one without a Tooth, and one cutting to the left.

Edward, It looks like you need to shift the upper rail to the left a couple of mm. A useful check is to take two down shots, rotating the head 180 degrees between them. Stitch them with control points only on the background and output a rectilinear view covering 50 degrees fov, say, as a layered PSD file. Display in Photoshop with reduced opacity on the upper layer - like this:

To get the centre of the images in register, you need to correct a horizontal offset with an adjustment to the lower rail setting. You can estimate the adjustment needed by reference to the scale markings, being half the measured distance between features in the two images. The vertical offset can be corrected by a rotational adjustment to the camera on its mount to the upper rail (unless it's fixed). Don't spend hours over this in a quest for perfection. Misalignments in the floor tiles may be more to do with your skills level in using PTGui than slight errors in the panorama head settings.